Methods for characterizing protein complexes

ABSTRACT

Methods for characterizing protein complexes formed between protein drug products and soluble ligands are provided herein. The disclosed methods can determine the size, heterogeneity, and conformation of protein complexes.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of and priority to U.S. ProvisionalPatent Application No. 62/724,700 filed on Aug. 30, 2018, which isincorporated by reference in its entirety.

TECHNICAL FIELD OF THE INVENTION

This invention is generally related to systems and methods ofcharacterizing protein complexes.

BACKGROUND OF THE INVENTION

Monoclonal antibodies (mAbs) are a growing therapeutic field, with over50 monoclonal antibodies currently on the market. Combination therapy ofmore than one monoclonal antibody has the potential to improve theefficacy of existing monotherapies. Certain soluble substances,particularly multimeric substances with several repeated epitopes, maybind with two or more antibodies, leading to the formation of largecomplexes. The production of large, heterogeneous antibody complexes isreferred to as “paper-dolling”. Large complexes of antibodies can berapidly eliminated by phagocytosis, leading to reduced efficacy of theantibody. Large protein complexes can also increase immunogenicity ofthe mAb.

Protein complexes can range in size from nanometer to visible particlesmaking their characterization by a single analytical techniquedifficult. One of the most widespread techniques used to determine thesize of particles from −1 nm to −1 μm is dynamic light scattering (DLS).DLS is an analytical technique used to determine protein sizedistribution profile, and is amenable to high throughput applications(Zhou, M., et al., Chem Med Chem, 11:738-756 (2016)). The Brownianmotion of proteins in solution causes light to be scattered, with theresultant scattered intensity fluctuations dependent on particle size.Thus, average radius and the width of the distribution in terms ofpolydispersity can be determined. However, DLS results are often biasedtowards larger particles and the particle populations must differ by afactor of at least three to be resolved. Therefore, DLS alone is notsufficient for analyzing protein complexes.

The high polydispersity of many aggregate samples requireseparation-based methods to provide more detailed information due to thewide size range of protein complexes. Size exclusion chromatography(SEC) is currently the most commonly used chromatographic technique forprotein separation (Brusotti, et al., Chromatographia, 81:3-23 (2018)).In SEC, separation occurs according to hydrodynamic volume or size ofmolecules. Smaller molecules are retained longer because they are ableto diffuse into the pores of the stationary phase, while largermolecules elute first because they are excluded from the pores. However,SEC is limited by upper molecular weight exclusion limits, sampleadsorption to the stationary phase, shear degradation at high pressuresand flow rates, and an inability to separate analytes based oncomposition.

Flow field-flow fractionation (FFF) is a promising alternative to SECwhen it comes to separation of large proteins and high molar masspolymers. FFF sample separation uses a flow-assisted separation andfractionation method in which the analytes are separated along a ribbonlike channel by differences in their diffusion coefficients (Fraunhofer,W. and Winter, G., Eur. J. Pharm. Biopharm, 58:369-383 (2004)). FFF canseparate analytes in a wide size range (from nanometers to microns). Theopen channel of FFF renders reduced sample loss, low pressures, and lowshear rates. While FFF has been used in combination with other moleculartechniques such as light scattering to detect protein aggregates, thereis still a growing need to more fully characterize heterogeneity andconformation of protein complexes, including mAb and soluble ligandcomplexes.

Therefore, it is an object of the invention to provide methods foridentifying protein drug products that have the ability to form largeprotein complexes.

It is another object of the invention to provide methods of identifyingand characterizing protein drug product and soluble ligand complexes.

SUMMARY OF THE INVENTION

Methods for characterizing protein complexes in a sample are provided.One embodiment provides a method for assessing the stoichiometry andsize distribution of protein complexes in a sample by fractionating thesample by asymmetrical flow field flow fractionation (A4F), anddetermining the stoichiometry and size distribution of the proteincomplexes in the sample using Multi-Angle Laser Light Scattering(MALLS). In some embodiments, the protein complexes contain an antibodyor fusion protein bound to its ligand. The ligand is typically a solubleligand. The ligand can be monomeric or multimeric. In one embodiment theligand can be a homodimer or heterodimer. In another embodiment theprotein complexes comprise or consist of antibody:ligand complexes orfusion protein:ligand complexes.

Another embodiment provides a method for selecting a lead protein drugproduct by adding a first protein drug product to a first samplecontaining a target or ligand of the first protein drug product toproduce protein:ligand complexes, and adding a second protein drugproduct to a second sample containing the target or ligand to formprotein:ligand complexes. The method includes separating theprotein:ligand complexes and determining the molar mass, stoichiometry,and size distribution of protein:ligand complexes using asymmetricalflow field flow fractionation—MALLS. The method also includes selectingthe protein drug product that forms fewer large protein:ligand complexesas the lead target protein drug. Typically, the protein drug product isan antibody or antigen binding fragment thereof, a fusion protein, or arecombinant protein. In some embodiments, the ligand is a solubleligand. The ligand can be monomeric or multimeric. In some embodimentsthe large protein complexes are heterometric.

Another embodiment provides a pharmaceutical composition containing thelead protein drug product selected using the method described above.

In some embodiments, the disclosed methods can be used to determine iftwo individual antibodies targeting the same ligand will form large,heterogeneous complexes.

Still another embodiment provides a method for characterizing proteincomplexes formed between protein drug products and soluble ligands bypreparing a sample containing the protein drug product and its ligand toproduct protein drug product:ligand complexes. The method includefractionating the protein drug:ligand complexes and analyzing thefractionated protein drug:ligand complexes by multi-angle laser lightscattering to determine the size and heterogeneity of protein complexes.In one embodiment, fractionating the total protein is performed byasymmetrical flow field flow fractionation. The concentration of theprotein can be determined with an additional step of UV/Vis.

The differences in conformation of protein complexes formed by differentprotein drug products to the same ligand can be determined by comparingthe elution profile/time of protein drug product:ligand complexes formedby the different protein drug products. Different elution profiles/timesof complexes with the same molar mass indicate that the complexes mayhave different conformations or shapes. In one embodiment, each proteindrug product and the same soluble ligand is analyzed separately in orderto calculate a theoretical molar mass for each individual component,wherein the theoretical molar mass is used to determine theheterogeneity of each protein complex.

Another embodiment provides a method for characterizing proteincomplexes formed between protein drug products and soluble ligands byfractionating protein drug product:ligand complexes using asymmetricalflow-field flow fractionation, analyzing the fractionated protein drugproduct:ligand complexes by multi-angle laser light scattering tocharacterize the size, stoichiometry, or both of protein drug:ligandcomplexes, and determining the heterogeneity of the protein complexes bycomparing the size of each protein complex to the theoretical size ofeach individual component to determine the components that make up eachcomplex.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is an illustration of a complex formed between one antibody andone ligand.

FIG. 1B is an illustration of a complex formed between one antibody andtwo ligands. FIG. 1C is an illustration of a complex formed between fourantibodies and five ligands, representative of “paper dolling”.

FIGS. 2A-2B are an illustration of a complex formed between antibody 1(black), two ligands, and antibody 2 (gray) in a non-linearconformation. FIGS. 2C-2D are an illustration of an complex formedbetween antibody 1 (black), two ligands, and antibody 2 (gray) in alinear conformation.

FIG. 3A is a chromatogram from SEC-MALLS analysis of Ab1, Protein X, andcombinations of Ab1 and Protein X at ratios of 5:1, 1:1, and 1:5. The Xaxis represents elution time (minutes). The left Y axis represents molarmass (g/mol) and the right Y axis represents absorbance at 280 nm (AU).FIG. 3B is a fractogram from A4F-MALLS analysis of combinations of Ab1and Ab2 at ratios of 5:1, 2:1, and 1:1. The X axis represents elutiontime (minutes). The left Y axis represents molar mass (g/mol). The rightY axis represents absorbance at 215 nm (AU).

FIG. 4A is a fractogram from A4F-MALLS analysis of lead compound A (LeadA), Lead A+Protein Y (1:3), and Lead compound B (Lead B)+Protein Y(1:3). FIG. 4B is a fractogram from A4F-MALLS analysis of Lead A, LeadA+Protein Y (1:1), and Lead B+Protein Y (1:1). FIG. 4C is a fractogramfrom A4F-MALLS analysis of Lead A, Lead A+Protein Y (3:1), and LeadB+Protein Y (3:1). The X axis represents time (minutes). The left Y axisrepresents molar mass (g/mol) and the right Y axis represents absorbanceat 280 nm (AU).

FIGS. 5A and 5B are line graphs of mouse anti-human antibody titer ofanti-Protein Y complexes with Lead A (FIG. 5A) and Lead B (FIG. 5B). TheX axis represents time (days) and the Y axis represents concentration(μg/ml).

FIGS. 6A and 6B are line graphs showing percent hemolysis of rabbit redblood cells with increasing concentrations of various anti-Protein ZmAbs (FIG. 6A) or combinations of Ab3 and various anti-Protein Z mAbs(FIG. 6B). The X axis represents concentration of mAb (Log [M]). The Yaxis represents percent hemolysis.

FIG. 7 is a fractogram from A4F-MALLS analysis of Free anti-Protein ZmAb1, Protein Z, and 1 μM:1 μM combination of anti-Protein Z mAb1 andProtein Z. The X axis represents elution time (minutes). The left Y axisrepresents molar mass (g/mol) and the right Y axis represents absorbanceat 215 nm (AU).

FIG. 8 is a fractogram from A4F-MALLS analysis of Free mAb, 1 μM:1 μMcombination of anti-Protein Z mAb1 and Protein Z, 0.5 μM:0.5 μM:1 μMcombination of anti-Protein Z mAb1, anti-Protein Z mAb5, and Protein Z,and 0.5 μM:0.5 μM:1 μM combination of anti-Protein Z mAb1, anti-ProteinZ mAb7, and Protein Z. The X axis represents elution time (minutes). Theleft Y axis represents molar mass (g/mol) and the right Y axisrepresents absorbance at 215 nm (AU).

FIG. 9 is a fractogram from A4F-MALLS analysis of Free mAb combo, 1 μM:1μM combination of anti-Protein Z mAb1 and Protein Z, 0.5 μM:0.5 μM:1 μMcombination of anti-Protein Z mAb1, anti-Protein Z mAb3 combo, andProtein Z, and 0.5 μM:0.5 μM:1 μM combination of anti-Protein Z mAb1,anti-Protein Z mAb6 combo, and Protein Z, and μM combination ofanti-Protein Z mAb1, anti-Protein Z mAb6/anti-Protein Z mAb7, andProtein Z. The X axis represents elution time (minutes). The left Y axisrepresents molar mass (g/mol) and the right Y axis represents absorbanceat 215 nm (AU).

FIG. 10 is a fractogram from A4F-MALLS analysis of free mAb combo, 1μM:1 μM combination of anti-Protein Z mAb1 and Protein Z, 0.5 μM:0.5μM:1 μM combination of anti-Protein Z mAb1, anti-Protein Z mAb2, andProtein Z, and 0.5 μM:0.5 μM:1 μM combination of anti-Protein Z mAb1,COMP1 mAb, and Protein Z. The X axis represents elution time (minutes).The left Y axis represents molar mass (g/mol) and the right Y axisrepresents absorbance at 215 nm (AU).

FIG. 11 is a fractogram from A4F-MALLS analysis of Free mAb combo, 1μM:1 μM combination of anti-Protein Z mAb1 and Protein Z, 0.5 μM:0.5μM:1 μM combination of anti-Protein Z mAb1, anti-Protein Z mAb4, andProtein Z. The X axis represents elution time (minutes). The left Y axisrepresents molar mass (g/mol) and the right Y axis represents absorbanceat 215 nm (AU).

FIGS. 12A and 12B are fractograms from A4F-MALLS analysis ofsimultaneous addition (FIG. 12A) or sequential addition (FIG. 12B) of0.3 μM:1 μM:1 μM anti-Protein Z mAb1:COMP1 mAb:Protein Z, 1 μM:1 μM:1 μManti-Protein Z mAb1:COMP mAb:Protein Z, and 3 μM:1 μM:1 μM anti-ProteinZ mAb1:COMP mAb:Protein Z. The X axis represents elution time (minutes).The left Y axis represents molar mass (g/mol) and the right Y axisrepresents absorbance at 215 nm (AU).

FIG. 13 is a fractogram from A4F-MALLS analysis of a representative mAb,Protein W, and combinations of mAb and Protein W at ratios of 1 μM:1 μM.The X axis represents elution time (minutes). The left Y axis representsmolar mass (g/mol) and the right Y axis represents absorbance at 215 nm(AU).

FIG. 14 is a fractogram from A4F-MALLS analysis of a representative mAb,Protein W, and combinations of mAb2 and Protein W, mAb3 and Protein W,and COMP1 and Protein W at ratios of 1 μM:1 μM. The X axis representselution time (minutes). The left Y axis represents molar mass (g/mol)and the right Y axis represents absorbance at 215 nm (AU).

FIG. 15 is a fractogram from A4F-MALLS analysis of COMP2, Protein W, andcombinations of COMP2 and Protein W at ratios of 1 μM:1 μM. The X axisrepresents elution time (minutes). The left Y axis represents molar mass(g/mol) and the right Y axis represents absorbance at 215 nm (AU).

FIG. 16 is a fractogram from A4F-MALLS analysis of a representative mAb,Protein W, and combinations of mAb4 and Protein W, and COMP3 and ProteinW at ratios of 1 μM:1 μM. The X axis represents elution time (minutes).The left Y axis represents molar mass (g/mol) and the right Y axisrepresents absorbance at 215 nm (AU).https://mccarterenglishllp.sharefile.com/d-s1dcf88b869fb404a9334563a10b04728

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

It should be appreciated that this disclosure is not limited to thecompositions and methods described herein as well as the experimentalconditions described, as such may vary. It is also to be understood thatthe terminology used herein is for the purpose of describing certainembodiments only, and is not intended to be limiting, since the scope ofthe present disclosure will be limited only by the appended claims.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure belongs. Although any compositions,methods and materials similar or equivalent to those described hereincan be used in the practice or testing of the present invention. Allpublications mentioned are incorporated herein by reference in theirentirety.

The use of the terms “a,” “an,” “the,” and similar referents in thecontext of describing the presently claimed invention (especially in thecontext of the claims) are to be construed to cover both the singularand the plural, unless otherwise indicated herein or clearlycontradicted by context.

Recitation of ranges of values herein are merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range, unless otherwise indicated herein, and eachseparate value is incorporated into the specification as if it wereindividually recited herein.

Use of the term “about” is intended to describe values either above orbelow the stated value in a range of approx. +/−10%; in otherembodiments the values may range in value either above or below thestated value in a range of approx. +/−5%; in other embodiments thevalues may range in value either above or below the stated value in arange of approx. +/−2%; in other embodiments the values may range invalue either above or below the stated value in a range of approx.+/−1%. The preceding ranges are intended to be made clear by context,and no further limitation is implied. All methods described herein canbe performed in any suitable order unless otherwise indicated herein orotherwise clearly contradicted by context. The use of any and allexamples, or exemplary language (e.g., “such as”) provided herein, isintended merely to better illuminate the invention and does not pose alimitation on the scope of the invention unless otherwise claimed. Nolanguage in the specification should be construed as indicating anynon-claimed element as essential to the practice of the invention.

“Protein” refers to a molecule comprising two or more amino acidresidues joined to each other by a peptide bond. Protein includespolypeptides and peptides and may also include modifications such asglycosylation, lipid attachment, sulfation, gamma-carboxylation ofglutamic acid residues, alkylation, hydroxylation and ADP-ribosylation.Proteins can be of scientific or commercial interest, includingprotein-based drugs, and proteins include, among other things, enzymes,ligands, receptors, antibodies and chimeric or fusion proteins. Proteinsare produced by various types of recombinant cells using well-known cellculture methods, and are generally introduced into the cell by geneticengineering techniques (e.g., such as a sequence encoding a chimericprotein, or a codon-optimized sequence, an intronless sequence, etc.)where it may reside as an episome or be intergrated into the genome ofthe cell.

“Antibody” refers to an immunoglobulin molecule consisting of fourpolypeptide chains, two heavy (H) chains and two light (L) chainsinter-connected by disulfide bonds. Each heavy chain has a heavy chainvariable region (HCVR or VH) and a heavy chain constant region. Theheavy chain constant region contains three domains, CH1, CH2 and CH3.Each light chain has a light chain variable region and a light chainconstant region. The light chain constant region consists of one domain(CL). The VH and VL regions can be further subdivided into regions ofhypervariability, termed complementarity determining regions (CDR),interspersed with regions that are more conserved, termed frameworkregions (FR). Each VH and VL is composed of three CDRs and four FRs,arranged from amino-terminus to carboxy-terminus in the following order:FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The term “antibody” includesreference to both glycosylated and non-glycosylated immunoglobulins ofany isotype or subclass. The term “antibody” includes antibody moleculesprepared, expressed, created or isolated by recombinant means, such asantibodies isolated from a host cell transfected to express theantibody. The term antibody also includes bispecific antibody, whichincludes a heterotetrameric immunoglobulin that can bind to more thanone different epitope. Bispecific antibodies are generally described inU.S. Pat. No. 8,586,713, which is incorporated by reference into thisapplication.

“Fc fusion proteins” comprise part or all of two or more proteins, oneof which is an Fc portion of an immunoglobulin molecule, which are nototherwise found together in nature. Preparation of fusion proteinscomprising certain heterologous polypeptides fused to various portionsof antibody-derived polypeptides (including the Fc domain) has beendescribed, e.g., by Ashkenazi et al., Proc. Natl. Acad. ScL USA 88:10535, 1991; Byrn et al., Nature 344:677, 1990; and Hollenbaugh et al.,“Construction of Immunoglobulin Fusion Proteins”, in Current Protocolsin Immunology, Suppl. 4, pages 10.19.1-10.19.11, 1992. “Receptor Fcfusion proteins” comprise one or more extracellular domain(s) of areceptor coupled to an Fc moiety, which in some embodiments comprises ahinge region followed by a CH2 and CH3 domain of an immunoglobulin. Insome embodiments, the Fc-fusion protein comprises two or more distinctreceptor chains that bind to a one or more ligand(s). For example, anFc-fusion protein is a trap, such as for example an IL-1 trap or VEGFtrap.

As used herein, “soluble ligand” refers to polar or charged ligands thatcannot readily cross the plasma membrane of a cell. Most soluble ligandsbind to the extracellular domains of cell-surface receptors.

“A4F” represents asymmetrical flow field-flow fractionation which is afractionating technique in which separation of analytes is achievedthrough the interaction of the sample with an external, perpendicularphysical field.

Multi angle light scattering (MALS) describes a technique for measuringthe light scattered by a sample into a plurality of angles. It is usedfor determining both the absolute molar mass and the average size ofmolecules in solution, by detecting how they scatter light. Collimatedlight from a laser source is most often used, in which case thetechnique can be referred to as multi angle laser light scattering(MALLS). In practice the terms MALS and MALLS are used interchangeably.

As used herein, “Brownian motion” refers to the continuous motion ofparticles suspended in liquid.

II. Methods for Characterizing Protein Complexes

Monoclonal antibody combination therapy has emerged as a promisingtherapeutic strategy for diseases such as cancer and inflammatoryconditions in which multiple signaling pathways are involved. Inaddition, administration of more than one monoclonal antibody targetingthe same pathway could be beneficial to completely block pathwaysinvolved in the pathogenesis of diseases when monotherapy alone does notfully inhibit the pathway. However, binding of therapeutic mAbs tosoluble, multimeric targets can lead to the formation of largeheterogeneous complexes. The size, shape, and conformation of a proteincomplex can affect immunogenicity and antibody clearance time, amongother factors. Analysis of protein complexes is important to provideinsight into the pharmacokinetics of a mAb during drug development.

Therefore, methods and systems for characterizing protein complexes areprovided. One embodiment provides a method for assessing thestoichiometry and size distribution of heterogeneous protein drugproduct:ligand complexes in a sample by fractionating the sample usingasymmetrical flow field flow fractionation and determining the molarmass, stoichiometry, and size distribution of heterogeneous proteincomplexes in the sample using multi-angle laser light scattering. Theprotein complexes typically are comprised of a protein that specificallybinds to a protein of interest also referred to as a target or ligand.In one embodiment the protein that specifically binds to the target isan antibody or fusion protein.

When an antibody or fusion protein is combined with its target or ligandin vivo or in vitro, a heterogeneous mixture of antibody:ligand orfusion protein:ligand can form. In one embodiment, binding oftherapeutic proteins such as monoclonal antibodies (mAbs) or fusionproteins to soluble, multimeric targets lead to large heterogeneouscomplexes or large heteromeric complexes. For example, the large proteincomplexes can be characterized as a protein complex with aprotein:ligand ratio selected from the group consisting of 3:2, 2:3,4:4, 6:6, or [2:2]_(n). Large heterogeneous complexes refer to complexesformed between multiple multimeric ligand molecules and multiple proteindrug product molecules. The term large heteromeric complex refers toligand bound by two different protein drug products, for example twodifferent antibodies, two different fusion proteins, or an antibody anda fusion protein binding the same ligand at different sites.

Another embodiment provides a method of identifying protein drugproducts that form large heterogeneous complexes with soluble targets invivo, in vitro, or both. The method includes preparing a samplecontaining a protein drug product and its soluble ligand to produceprotein drug product:ligand complexes, fractionating the sample toseparate the protein drug product:ligand complexes and analyzing thefractionated protein drug product:ligand complexes by multi-angle laserlight scattering to determine the size and heterogeneity of proteincomplexes. In one embodiment, the protein sample is fractionated usingasymmetrical flow field-flow fractionation.

Further details of the disclosed methods and systems are provided below.

A. System for Characterizing Protein Complexes

In one embodiment, the system includes an asymmetrical flow field-flowfractionation (A4F) system and a multi-angle laser light scattering(MALLS) system. An example of a commercially available A4F system is anEclipse™ 3+ A4F Separation System. An example of a commerciallyavailable MALLS system is the Wyatt Technology Dawn HELEOS® II laserlight scattering instrument. The system typically includes a UV/VISdetector and/or a refractive index detector. An exemplary commerciallyavailable UV/VIS detector is Agilent 1260 Infinity UV detector. Anexemplary commercially available refractive index detector is Optilab®T-rEX refractive index detector. In one embodiment the A4F systemincludes an A4F short channel fitted with a 350 W spacer and a 4 kDaMWCO NADIR® hydrophilic PES (PESH) membrane. In another embodiment, theA4F short channel is fitted with a 490 W spacer and a 10 kDa MWCO Nadir®regenerated cellulose membrane. Exemplary mobile phases include 10 mMphosphate and 500 mM NaCl at pH 7.0. However, an advantage of A4F overcolumn chromatography separation is that there are no limitations on thetype of mobile phase, or carrier fluid that can be used. In oneembodiment, the samples are separated using a linear gradient over 60minutes. In one embodiment, the channel flow and cross-flow program arespecifically optimized to achieve a desired resolution on a case-by-casebasis. It is to be understood that a person of skill in the art couldmodify and optimize the elution profile according to the resolutionbeing required of the specific sample being separated using A4F.

Typically, the sample is injected into the sample inlet port of the A4Fchannel. The sample is then focused by allowing the carrier fluid toflow into the channel from both the inlet and outlet ports, meeting at apoint in the channel, typically near the sample inlet port, to form afocusing zone. During the focusing period, particles from the injectedsample are held in this focusing zone to allow for relaxation prior tofractionation. The final step is fractionation of the particles. Asparticles flow along the channel, the perpendicularly-opposed cross-flowseparation field pushes the molecules towards the bottom of the channel.As they accumulate near the bottom of the channel, they undergo acounter acting diffusion back into the channel against the cross-flowfield. The extent to which the molecules can diffuse back into thechannel is dictated by their natural Brownian motion, a characteristicdefined by the translational diffusion coefficient, which, in turn, isrelated to the size and shape unique to each individual species.Generally, smaller particles have a faster diffusion coefficient thanlarger ones and are able to diffuse higher into the channel against thecross-flow field. The rate of laminar flow within the channel is notuniform. It travels in a parabolic pattern with the speed of the flowincreasing towards the center of the channel and decreasing towards theupper and lower walls of the channel. Therefore, the rate at whichparticles will be carried through will depend on their position withinthe channel. Those with faster diffusion, located near the center of thechannel, will be transported with a greater velocity. The largerparticles in the shallow, slower moving stream near the bottomaccumulation wall of the channel are transported with lower flowvelocity and elute later than smaller particles. This results in agentle separation of particles based on mass with the elution order ofsmallest to largest.

As the sample is flowing through the A4F channel, the leading portion ofsample exits the channel through an outlet port. The multi-angle laserlight scattering (MALLS) detector is in fluid communication with the A4Fsystem and receives sample from the A4F outlet port. In someembodiments, the sample first flows through a UV/VIS detector to measuresample concentration as a function of absorbance. The MALLS systemfocuses a beam of polarized light (or a laser) onto the sample moleculeand the scattered light is detected with a photo detector.

Multi angle light scattering (MALS) measures light being scattered froma sample containing molecules, particles, or protein complexes. Thisscattering depends on the optical configuration of the setup, and in atypical experimental realization, the light is then detected at one orseveral different angles. In the one-scattering-angle solution, thethree most popular designs are 90 degrees (also right angle lightscattering or RALS), 7 degrees (also low angle light scattering orLALS), or 173 degrees (also non-invasive back scattering or NIBS). Inthe multi-angle setup there are in principle those where the angles arefixed (this is most often called the MALS or MALLS setup) and thosewhere the angles are variable (typically referred to as a lightscattering goniometer or spectrometer). MALS usually refers to a systemwith multiple fixed angles used as part of a particle separation setup,for example A4F. The most widespread application of MALS is as anabsolute molar mass detector in conjunction with a concentrationdetector (like RI or single-wavelength UV).

MALS can be used to measure: M_(w)—weight-averaged molar mass of aprotein complex; R_(g)—average radius of protein complex; andA₂—solubility of protein in solution.

B. Methods of Characterizing Protein Complexes

The disclosed systems and methods can be used to characterize proteincomplexes, for example protein drug product:ligand complexes in asample. One embodiment provides a method for assessing the stoichiometryand size distribution of heterogeneous protein complexes in a sample byfractionating the sample by asymmetrical flow field flow fractionation(A4F), and determining the molar mass, stoichiometry and sizedistribution of protein complexes in the sample using Multi-Angle LaserLight Scattering (MALLS), wherein the complexes comprise or consist ofantibody:ligand complexes or fusion protein:ligand complexes. In someembodiments, the ligand is a soluble ligand. Typically, the antibody isa monoclonal antibody. In one embodiment, the protein complex ischaracterized by its antibody or fusion protein to ligand ratio. In anon-limiting example, the antibody or fusion protein to ligand ratio canbe selected from the group consisting of 1:0, 0:1, 1:1, 1:2, 2:1, 2:2,3:2, 2:3, 4:4, 6:6, or [2:2]_(n). It is to be understood that theantibody or fusion protein to ligand ratio will be dependent on thespecific antibody or fusion protein and ligand that are being tested.

1. Mixtures of Protein Complexes

To determine the characteristics of protein complexes, a theoreticalmass can be determined for each component of the complex. In oneembodiment, each protein and ligand in the mixture is analyzedseparately to determine a theoretical molar mass for each component. Inone embodiment, a protein drug product and its ligand are mixed to formprotein drug product:ligand complexes and the complexes are thencharacterized. The fractionated protein drug product:ligands aresubjected to A4F-MALLS to determine molar mass of the complexes. Themasses of the complexes are then compared to the theoretical molar massof the individual components to determine the likely stoichiometricratio of individual components present in each complex. In oneembodiment, the methods can detect a 1:1 protein drug product:ligandcomplex. In another embodiment, the methods can detect any ratio ofprotein drug product:ligand. In a non-limiting example, the methods candetect a protein drug product:ligand complex of 1:0, 0:1, 2:1, 1:2, 2:2,3:2, 2:3, 4:4, 6:6, or [2:2]_(n). It is to be understood that theantibody or fusion protein to ligand ratio will be dependent on thespecific antibody or fusion protein and ligand that are being tested. Insome embodiments, the complex contains multiple different protein drugproducts complexed with a common soluble ligand.

a. Ligands

The ligand in the protein drug product:ligand complex can be a monomericor multimeric ligand. In one embodiment, the ligand is a soluble ligand.In some embodiments the soluble ligands correspond to the extracellularportions of transmembrane proteins including but not limited totransmembrane receptor proteins.

Monomeric ligands contain only one protein or one protein unit.Multimeric ligands can be for example dimeric, trimeric, etc. containingmultiple proteins or protein subunits. For example the ligands can behomodimers or heterodimers. In some embodiments, the multimeric ligandsbind to more than one molecule of a protein drug product. FIG. 1A showsan exemplary 1:1 antibody:ligand complex. FIG. 1B shows an exemplary 1:2antibody:ligand complex, and FIG. 1C shows an example of the “paperdolling” effect wherein each arm of an interior antibody binds to adifferent ligand creating a large, heterogeneous complex.

In one embodiment, the large, heterogeneous protein drug product:ligandcomplex has a size of 500 kDa or greater. In another embodiment, theheterogeneous protein drug product:ligand complex has a size of 500-4000kDa. In another embodiment, the large, heterogeneous protein drugproduct:ligand has a ratio of protein drug product:ligand of 3:2, 2:3,4:4, or 6:6.

In one embodiment, the disclosed methods are used to determine if a leadprotein drug product designed to target a multimeric ligand will formlarge, heterogeneous protein drug product:ligand complexes.

In one embodiment, the disclosed methods can be used to determine if amultimeric ligand will form complexes with more than one protein drugproduct or fusion protein. The complexes that can be formed include butare not limited to protein:ligand ratios of 1:0, 0:1, 2:1, 1:2, 2:2,3:2, 2:3, 4:4, 6:6, or [2:2]_(n). FIGS. 1A-1C illustrate exemplarycomplexes that could be formed between a multimeric ligand and amonoclonal antibody.

b. Combination of Multiple mAbs

Combination therapy using multiple protein drug products to target thesame pathway or the same ligand is growing in popularity. In someembodiments, the disclosed methods can be used to distinguish betweendifferent combinations of antibodies targeting the same ligand based onthe stoichiometry and size distributions of protein complexes formed bythe protein drug products. When two protein drug products are mixedtogether with a monomeric ligand, the protein drug products have thepotential to form a heteromeric complex. A heteromeric complex, asdefined herein, refers to two different protein drug products bindingthe same target molecule. In addition, each of the two arms of the sameantibody have the ability to bind two ligands which can also be bound bya second antibody to form a heteromeric complex. FIGS. 2A-2D showrepresentative heteromeric complexes. FIGS. 2A and 2C show complexesformed when one protein drug product (black), or antibody, binds twoligands and one of the ligands is also bound by a second, unique proteindrug product (gray). If the gray protein is bound by another ligandwhich is then bound by the black protein, larger, more heterogeneouscomplexes can form, as represented in FIGS. 2B and 2D.

2. Selecting Lead Protein Drug Product

Another embodiment provides a method for selecting a lead protein drugproduct by adding a first protein drug product to a first samplecomprising a target of the first protein drug product to produceheterogeneous protein:ligand complexes and adding a second protein drugproduct to the a second sample containing the target to formprotein:ligand complexes. The method includes separating theheterogeneous protein:ligand complexes and determining the sizedistribution and stoichiometry of heterogeneous protein:ligand complexesusing Asymmetrical flow field flow fractionation—Multi-Angle Laser LightScattering. The methods also include selecting the protein drug productthat forms fewer heterogeneous protein:ligand complexes as the leadtarget protein drug. In some embodiments, the ligand is a solubleligand. The soluble ligand can be a monomeric ligand or a multimericligand. Typically, the protein drug product is an antibody or antigenbinding fragment thereof, a fusion protein, or a recombinant protein.The protein complex can be characterized as a protein complex with anantibody or fusion protein to ligand ratio selected from the groupconsisting of but not limited to 1:0, 0:1, 1:1, 1:2, 2:1, 2:2, 3:2, 2:3,4:4, 6:6, or [2:2]_(n). Another embodiment provides a pharmaceuticalcomposition containing the lead protein drug product selected using themethod above.

3. Determining Size and Shape of Protein Complexes

In one embodiment, the disclosed methods can be used to determine thesize of protein complexes. A mixture of protein drug products, andoptionally soluble ligands, are separated using an A4F fractionation.The size and stoichiometry of the protein complexes can then bedetermined using MALLS analysis. In MALLS analysis, a beam of polarizedlight (or a laser) is focused onto the sample molecule and the scatteredlight is detected with a photo detector. The scattered light is detectedat various different angles simultaneously. The intensity of thescattered light at each angle is proportional to the molar mass of thecomplex. In one embodiment, UV/Vis spectrometry is used to determine theconcentration of each protein complex.

In another embodiment, the shape/conformation of a protein complexformed between different protein drug products to a common ligand can bedistinguished using the disclosed methods. Differences in elution timeor elution profile between complexes with the same molar mass suggestdifferences in shape or conformation of the protein complexes. Complexeswith the same or similar molar mass but with different elution timesindicate that the complex with the slower elution time has an increasedhydrodynamic volume due to a difference in shape or conformation of thecomplex.

The size and heterogeneity of the protein complexes can be used topredict the clearance of the protein drug product. In one embodiment,the larger the protein complex, the faster the protein drug product iscleared from the body.

C. Proteins in the Protein Complexes

In one embodiment one of the proteins in the protein complex is aprotein drug product or is a protein of interest suitable for expressionin prokaryotic or eukaryotic cells. For example, the protein in theprotein complexes can be an antibody or antigen-binding fragmentthereof, a chimeric antibody or antigen-binding fragment thereof, anScFv or fragment thereof, an Fc-fusion protein or fragment thereof, agrowth factor or a fragment thereof, a cytokine or a fragment thereof,or an extracellular domain of a cell surface receptor or a fragmentthereof. Proteins in the complexes may be simple polypeptides consistingof a single subunit, or complex multisubunit proteins comprising two ormore subunits. The protein of interest may be a biopharmaceuticalproduct, food additive or preservative, or any protein product subjectto purification and quality standards.

In some embodiments, the protein in the protein complexes is anantibody, a human antibody, a humanized antibody, a chimeric antibody, amonoclonal antibody, a multispecific antibody, a bispecific antibody, anantigen binding antibody fragment, a single chain antibody, a diabody,triabody or tetrabody, a dual-specific, tetravalent immunoglobulinG-like molecule, termed dual variable domain immunoglobulin (DVD-IG), anIgD antibody, an IgE antibody, an IgM antibody, an IgG antibody, an IgG1antibody, an IgG2 antibody, an IgG3 antibody, or an IgG4 antibody. Inone embodiment, the antibody is an IgG1 antibody. In one embodiment, theantibody is an IgG2 antibody. In one embodiment, the antibody is an IgG4antibody. In another embodiment, the antibody comprises a chimerichinge. In still other embodiments, the antibody comprises a chimeric Fc.In one embodiment, the antibody is a chimeric IgG2/IgG4 antibody. In oneembodiment, the antibody is a chimeric IgG2/IgG1 antibody. In oneembodiment, the antibody is a chimeric IgG2/IgG1/IgG4 antibody.

In some embodiments, the antibody is selected from the group consistingof an anti-Programmed Cell Death 1 antibody (e.g. an anti-PD1 antibodyas described in U.S. Pat. Appln. Pub. No. US2015/0203579A1), ananti-Programmed Cell Death Ligand-1 (e.g., an anti-PD-L1 antibody asdescribed in in U.S. Pat. Appln. Pub. No. US2015/0203580A1), ananti-D114 antibody, an anti-Angiopoetin-2 antibody (e.g., an anti-ANG2antibody as described in U.S. Pat. No. 9,402,898), ananti-Angiopoetin-Like 3 antibody (e.g., an anti-AngPt13 antibody asdescribed in U.S. Pat. No. 9,018,356), an anti-platelet derived growthfactor receptor antibody (e.g., an anti-PDGFR antibody as described inU.S. Pat. No. 9,265,827), an anti-Erb3 antibody, an anti-ProlactinReceptor antibody (e.g., anti-PRLR antibody as described in U.S. Pat.No. 9,302,015), an anti-Complement 5 antibody (e.g., an anti-05 antibodyas described in U.S. Pat. Appln. Pub. No US2015/0313194A1), an anti-TNFantibody, an anti-epidermal growth factor receptor antibody (e.g., ananti-EGFR antibody as described in U.S. Pat. No. 9,132,192 or ananti-EGFRvIII antibody as described in U.S. Pat. Appln. Pub. No.US2015/0259423A1), an anti-Proprotein Convertase Subtilisin Kexin-9antibody (e.g., an anti-PCSK9 antibody as described in U.S. Pat. No.8,062,640 or U.S. Pat. No. 9,540,449), an Anti-Growth andDifferentiation Factor-8 antibody (e.g. an anti-GDF8 antibody, alsoknown as anti-myostatin antibody, as described in U.S. Pat. No.8,871,209 or 9,260,515), an anti-Glucagon Receptor (e.g. anti-GCGRantibody as described in U.S. Pat. Appln. Pub. Nos. US2015/0337045A1 orUS2016/0075778A1), an anti-VEGF antibody, an anti-IL1R antibody, aninterleukin 4 receptor antibody (e.g., an anti-IL4R antibody asdescribed in U.S. Pat. Appln. Pub. No. US2014/0271681A1 or U.S. Pat. No.8,735,095 or 8,945,559), an anti-interleukin 6 receptor antibody (e.g.,an anti-IL6R antibody as described in U.S. Pat. No. 7,582,298, 8,043,617or 9,173,880), an anti-IL1 antibody, an anti-IL2 antibody, an anti-IL3antibody, an anti-IL4 antibody, an anti-IL5 antibody, an anti-IL6antibody, an anti-IL7 antibody, an anti-interleukin 33 (e.g., anti-IL33antibody as described in U.S. Pat. No. 9,453,072 or 9,637,535), ananti-Respiratory syncytial virus antibody (e.g., anti-RSV antibody asdescribed in U.S. Pat. No. 9,447,173), an anti-Cluster ofdifferentiation 3 (e.g., an anti-CD3 antibody, as described in U.S. Pat.Nos. 9,447,173 and 9,447,173, and in U.S. Application No. 62/222,605),an anti-Cluster of differentiation 20 (e.g., an anti-CD20 antibody asdescribed in U.S. Pat. No. 9,657,102 and US20150266966A1, and in U.S.Pat. No. 7,879,984), an anti-CD19 antibody, an anti-CD28 antibody, ananti-Cluster of Differentiation-48 (e.g. anti-CD48 antibody as describedin U.S. Pat. No. 9,228,014), an anti-Fel d1 antibody (e.g. as describedin U.S. Pat. No. 9,079,948), an anti-Middle East Respiratory Syndromevirus (e.g. an anti-MERS antibody as described in U.S. Pat. Appln. Pub.No. US2015/0337029A1), an anti-Ebola virus antibody (e.g. as describedin U.S. Pat. Appln. Pub. No. US2016/0215040), an anti-Zika virusantibody, an anti-Lymphocyte Activation Gene 3 antibody (e.g. ananti-LAG3 antibody, or an anti-CD223 antibody), an anti-Nerve GrowthFactor antibody (e.g. an anti-NGF antibody as described in U.S. Pat.Appln. Pub. No. US2016/0017029 and U.S. Pat. Nos. 8,309,088 and9,353,176) and an anti-Protein Y antibody. In some embodiments, thebispecific antibody is selected from the group consisting of ananti-CD3×anti-CD20 bispecific antibody (as described in U.S. Pat. Appln.Pub. Nos. US2014/0088295A1 and US20150266966A1), an anti-CD3×anti-Mucin16 bispecific antibody (e.g., an anti-CD3×anti-Muc16 bispecificantibody), and an anti-CD3×anti-Prostate-specific membrane antigenbispecific antibody (e.g., an anti-CD3×anti-PSMA bispecific antibody).In some embodiments, the protein of interest is selected from the groupconsisting of abciximab, adalimumab, adalimumab-atto, ado-trastuzumab,alemtuzumab, alirocumab, atezolizumab, avelumab, basiliximab, belimumab,benralizumab, bevacizumab, bezlotoxumab, blinatumomab, brentuximabvedotin, brodalumab, canakinumab, capromab pendetide, certolizumabpegol, cemiplimab, cetuximab, denosumab, dinutuximab, dupilumab,durvalumab, eculizumab, elotuzumab, emicizumab-kxwh,emtansinealirocumab, evinacumab, evolocumab, fasinumab, golimumab,guselkumab, ibritumomab tiuxetan, idarucizumab, infliximab,infliximab-abda, infliximab-dyyb, ipilimumab, ixekizumab, mepolizumab,necitumumab, nesvacumab, nivolumab, obiltoxaximab, obinutuzumab,ocrelizumab, ofatumumab, olaratumab, omalizumab, panitumumab,pembrolizumab, pertuzumab, ramucirumab, ranibizumab, raxibacumab,reslizumab, rinucumab, rituximab, sarilumab, secukinumab, siltuximab,tocilizumab, tocilizumab, trastuzumab, trevogrumab, ustekinumab, andvedolizumab.

In some embodiments, the protein in the complexes is a recombinantprotein that contains an Fc moiety and another domain, (e.g., anFc-fusion protein). In some embodiments, an Fc-fusion protein is areceptor Fc-fusion protein, which contains one or more extracellulardomain(s) of a receptor coupled to an Fc moiety. In some embodiments,the Fc moiety comprises a hinge region followed by a CH2 and CH3 domainof an IgG. In some embodiments, the receptor Fc-fusion protein containstwo or more distinct receptor chains that bind to either a single ligandor multiple ligands. For example, an Fc-fusion protein is a TRAPprotein, such as for example an IL-1 trap (e.g., rilonacept, whichcontains the IL-1RAcP ligand binding region fused to the Il-1R1extracellular region fused to Fc of hIgG1; see U.S. Pat. No. 6,927,004,which is herein incorporated by reference in its entirety), or a VEGFtrap (e.g., aflibercept or ziv-aflibercept, which comprises the Igdomain 2 of the VEGF receptor Flt1 fused to the Ig domain 3 of the VEGFreceptor Flk1 fused to Fc of hIgG1; see U.S. Pat. Nos. 7,087,411 and7,279,159). In other embodiments, an Fc-fusion protein is aScFv-Fc-fusion protein, which contains one or more of one or moreantigen-binding domain(s), such as a variable heavy chain fragment and avariable light chain fragment, of an antibody coupled to an Fc moiety.

EXAMPLES Example 1: A4F Analysis Offers Superior Resolution for SamplesContaining Large, Heterogeneous Complexes Compared to SEC FractionationMethods

SEC-MALLS Mobile Phase Buffer

The mobile phase buffer (10 mM sodium phosphate, 500 mM sodium chloride,pH 7.0±0.1) was prepared by combining 4.23 g sodium phosphate monobasicmonohydrate, 5.20 g sodium phosphate dibasic heptahydrate, and 500 mL 5M sodium chloride; the solution was then brought to a volume to 5.0 Lwith HPLC grade water. The final measured pH of the buffer was 7.0. Themobile phase buffer was filtered (0.2 μm) before use.

SEC-MALLS Analysis

The SEC-MALLS system is composed of a Superose 6 GL column (10 mm×300mm; GE Healthcare, cat #17-5172-01), coupled to an Agilent 1200 SeriesHPLC system equipped with a ultraviolet (UV) diode array detector, WyattTechnology miniDawn TREOS® laser light scattering instrument (LS), andan Optilab® T-rEX differential refractometer (RI) detector. Thedetectors were connected in series in the following order: UV-LS-RI. LSand RI detectors were calibrated according to instructions provided byWyatt Technology.

Defined amounts of anti-ProteinX mAb were each combined with recombinantProteinX and diluted in 1×DPBS, pH 7.4 to yield the following molarratios: 5 μM anti-ProteinX mAb: 1 μM ProteinX, 1 μM anti-ProteinX mAb: 1μM ProteinX, and 1 μM anti-ProteinX mAb: 5 μM ProteinX. All samples wereincubated at ambient temperature for 2 hours and maintained unfilteredat 4° C. prior to injection into the column. The column waspre-equilibrated with the mobile phase buffer (10 mM sodium phosphate,500 mM sodium chloride, pH 7.0±0.1) at a flow rate of 0.3 mL/min, priorto the injection of each sample. Bovine serum albumin (BSA; 2 mg/mL; 150μg sample load) was injected separately and included as a systemsuitability control.

The SEC-MALLS mobile phase buffer (10 mM sodium phosphate, 500 mM sodiumchloride, pH 7.0±0.1) was used throughout the fractionation. Each sample(100-200 μg) was injected, and was eluted with a flow rate of 0.3mL/min. BSA was fractionated using the same parameter settings.

A4F-MALLS Mobile Phase Buffer

The mobile phase buffer (10 mM sodium phosphate, 500 mM sodium chloride,pH 7.0±0.1) was prepared by combining 4.23 g sodium phosphate monobasicmonohydrate, 5.20 g sodium phosphate dibasic heptahydrate, and 500 mL 5M sodium chloride; the solution was then brought to a volume to 5.0 Lwith HPLC grade water. The final measured pH of the buffer was 7.0. Themobile phase buffer was filtered (0.2 μm) before use.

A4F-MALLS

The A4F-MALLS system was composed of an Eclipse™ 3+A4F Separation Systemcoupled to an Agilent 1200 Series HPLC system equipped with aultraviolet (UV) diode array detector, Wyatt Technology Dawn HELEOS® IIlaser light scattering instrument (LS), and an Optilab® T-rEXdifferential refractometer (RI) detector. The detectors were connectedin series in the following order: UV-LS-RI. LS and RI detectors werecalibrated according to instructions provided by Wyatt Technology.

Defined amounts of anti-ProteinX mAb were each combined with recombinantProteinX and diluted in 1×DPBS, pH 7.4 to yield the following molarratios: 5 μM anti-ProteinX mAb: 1 μM ProteinX, 2 μM anti-ProteinX mAb: 1μM ProteinX, and 1 μM anti-ProteinX mAb: 1 μM ProteinX. All samples wereincubated at ambient temperature for 2 hours and maintained unfilteredat 4° C. prior to injection into an Eclipse™ short channel fitted with aW350 spacer foil (350 μm spacer thickness, 2.2 cm spacer width) andusing a 10 kDa MWCO Nadir regenerated cellulose membrane. The channelwas pre-equilibrated with the mobile phase buffer (10 mM sodiumphosphate, 500 mM sodium chloride, pH 7.0±0.1), prior to the injectionof each sample. Bovine serum albumin (BSA; 2 mg/mL; 10 μg sample load)was injected separately and included as a system suitability control.

The fractionation method consisted of four steps: injection, focusing,elution, and a channel “wash-out” step. The A4F-MALLS mobile phasebuffer (10 mM sodium phosphate, 500 mM sodium chloride, pH 7.0±0.1) wasused throughout the fractionation method. Each sample (7 μg) wasinjected at a flow rate of 0.2 mL/min for 1 min and subsequently focusedfor 2 min with a focus flow rate of 1.5 mL/min. The sample was elutedwith a channel flow rate of 1.0 mL/min with the linear gradient crossflow from 3.0 mL/min to 0 mL/min over 45 min. Finally, the cross flowwas held at 0 mL/min for an additional 5 min to wash out the channel.BSA was fractionated using the same parameter settings.

MALLS Data Analysis

Data were analyzed using ASTRA V software (version 5.3.4.14, WyattTechnology). The data were fit to the equation that relates the excessscattered light to the solute concentration and weight-average molarmass, Mw, (Wyatt, 1993; Kendrick, 2001)

$\begin{matrix}{\frac{K*c}{R\left( {\theta,c} \right)} = {\frac{1}{{MwP}(\theta)} + {2A_{2}c}}} & {{Equation}1}\end{matrix}$

-   -   where c is the solute concentration, R(θ,c) is the excess        Raleigh ratio from the solute as a function of scattering angle        and concentration, Mw is the molar mass, P(θ) describes the        angular dependence of scattered light (˜1 for particles with        radius of gyration <50 nm), A₂ is the second virial coefficient        in the expansion of osmotic pressure (which can be neglected        since measurements are performed on dilute solutions) and

$\begin{matrix}{K*={\frac{4\pi^{2}n_{0}^{2}}{N_{A}\lambda_{0}^{4}}\left( \frac{dn}{dc} \right)^{2}}} & {{Equation}2}\end{matrix}$

-   -   where n_(o) represents the solvent refractive index, NA is        Avogadro's number, λ₀ is the wavelength of the incident light in        a vacuum, and dn/dc represents the specific refractive index        increment for the solute.

The molar mass of BSA monomer served to evaluate the calibrationconstants of the light scattering and differential refractive indexdetectors during data collection (system suitability check). Therelative standard deviation (% RSD) of the average molar mass of BSAdetermined from the UV and RI detectors was ≤5.0%.

The normalization coefficients for the light scattering detectors,inter-detector delay volume and band broadening terms were calculatedfrom the BSA chromatograms collected for the A4F-MALLS conditionemployed. These values were applied to the data files collected for allthe other samples to correct for these terms.

The dn/dc value and the extinction coefficient at 215 nm or 280 nm(corrected for glycosylation) were experimentally determined using theprotein conjugate analysis provided in the Astra software. The correctedextinction coefficient and dn/dc value was used to analyze allprotein-protein complex samples.

Results

SEC-MALLS analysis of the samples showed poor resolution of higher ordercomplexes (elution volume=8-14 mL) and no distinction of intermediatecomplexes (FIG. 3A, Table 1). In contrast, A4F-MALLS analysis of thesamples showed superior resolution of higher order complexes (elutionvolume=˜11-30 mL) and clear distinction of intermediate complexes (FIG.3B, Table 2).

TABLE 1 Approximate molar mass and retention time for mAb:Protein Xcomplexes. Peak 2 Peak 3 Peak 4 Peak 1 [Intact Antibody]₂: [IntactAntibody]₁: [Intact Antibody]₁: Molar Higher Order [ProteinX]₁[ProteinX]₁ [ProteinX]₂ Ratio Complexes Complex Complex Complex Sample(mol:mol) R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w),kDa R_(t), min M_(w), kDa mAb1:ProteinX 5:1 9.0-12.6 ~390- 13.1 330.7 NANA NA NA 1000 mAb1:ProteinX 1:1 8.0-13.4 ~400- NA NA 15.4 166.9 NA NA3000 mAb1:ProteinX 1:5 8.5-13.8 ~430- NA NA NA NA 16.0 216.3 2000 R_(t):Retention Time; M_(w): weight average molar mass; NA: Not Applicable;min: minutes; kDa: kiloDaltons;

TABLE 2 Approximate molar mass and retention time for mAb:Protein Xcomplexes Peak 1 Peak 2 Peak 3 Peak 4 [Intact [Intact [Intact [IntactAntibody]₁: Antibody]₂: Antibody]₃: Antibody]₄: Peak 5 Molar[ProteinX]₁₋₂ [ProteinX] [ProteinX]₂ [ProteinX]₃ Higher Order RatioComplex Complex Complex Complex Complexes Sample (mol:mol) R_(t), minM_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w),kDa Sample (mol:mol) mAb1:ProteinX 5:1 NA NA 10.8 321.1 12.4 497.8 13.7673.8 14.6 830- 1190 mAb1:ProteinX 1:1 NA NA 10.7 332.8 12.5 514.8 13.7671.3 14.6 780- 1620 mAb1:ProteinX 1:5 9.4 191.1 NA NA 11.8 461.1 13.3599.7 14.4 720- 1180 R_(t): Retention Time; M_(w): weight average molarmass; NA: Not Applicable; min: minutes; kDa: kiloDaltons;

Example 2: Anti-Protein Y Complexes Methods

A4F MALLS Mobile Phase Buffer

1×DPBS, pH 7.4, was prepared by diluting 500 mL of 10×DPBS with HPLCgrade water to a total volume of 4.9 L. A solution of 0.0025% (w/v)sodium azide was added as an antimicrobial agent. Hydrochloric acid (12M) was slowly added in small volume increments to adjust the pH to 7.4before bringing the final volume to 5.0 L. The final, measured pH of thebuffer was 7.4. The buffer solution was prepared fresh and filtered (0.2μm) prior to use.

A4F MALLS Analysis

Defined amounts of anti-Protein Y mAbs (Lead A and Lead B) were eachcombined with recombinant human Protein Y and diluted in 1×DPBS, pH 7.4to yield the following molar ratios: 1 μM anti-Protein Y mAb: 3 μMhActA, 1 μM anti-Protein Y mAb: 1 μM Protein Y, and 3 μM anti-Protein YmAb: 1 μM Protein Y. All samples were incubated at ambient temperaturefor 2 hours and maintained unfiltered at 4° C. prior to injection intoan Eclipse™ short channel fitted with a W490 spacer foil (490 μm spacerthickness, 2.2 cm spacer width) and using a 10 kDa MWCO Nadirregenerated cellulose membrane. The channel was pre-equilibrated with1×DPBS buffer, pH 7.4, prior to the injection of each sample. Bovineserum albumin (BSA; 2 mg/mL; 10 μg sample load) was injected separatelyand included as a system suitability control.

The fractionation method consisted of four steps: injection, focusing,elution, and a channel “wash-out” step. The A4F-MALLS mobile phasebuffer (1×DPBS, pH 7.4) was used throughout the fractionation method.Each sample (10 μg) was injected at a flow rate of 0.2 mL/min for 1 minand subsequently focused for 2 min with a focus flow rate of 1.5 mL/min.The sample was eluted with a channel flow rate of 1.0 mL/min with thelinear gradient cross flow from 1.2 mL/min to 0 mL/min over 20 min.Finally, the cross flow was held at 0 mL/min for an additional 5 min towash out the channel. BSA was fractionated using the same parametersettings.

Mouse Anti-Human Antibody Titer

Mouse anti-human antibody (MAHA) titers were determined using a sandwichELISA specific for the detection of mAb A or mAb B mouse IgG. Briefly,mAb A or mAb B at 1 μg/mL in phosphate-buffered saline (PBS) werepassively adsorbed to a microtiter plate overnight at 4° C. followed bya nonspecific binding block with 5% bovine serum albumin (BSA) in PBS.Serial dilutions of serum samples were prepared in dilution buffer (0.5%BSA in PBS) starting from 1:100. Therefore, the corresponding dilutionfactor (100) was defined as the assay's lower limit of detection (LOD).Samples were then added to the mAb A or mAb B coated plate (100 μL/well)and incubated 16-18 hours at 4° C. Wells with addition of dilutionbuffer only were included to determine background signal. Subsequently,plate-captured mAb A or mAb B-specific MAHA was detected usinghorseradish peroxidase (HRP)-conjugated anti-mouse Fcγ at 40 ng/mL. Thechromogenic HRP-substrate, 3,3′,5,5′-tetramethylbenzidine (TMB) was usedto detect HRP activity; and the resultant optical density at 450 nm(OD₄₅₀) was read on a Perkin Elmer Victor X4 Multimode Plate Reader.Data of binding signal versus dilution factor were analyzed bynon-linear regression using GraphPad Prism software and titers werecalculated. The MAHA titer was defined as the calculated dilution factorof the serum sample corresponding to a binding signal equivalent totwice the background signal of the assay.

Results

The two lead mAbs formed distinctly different complexes with Protein Y.Under all conditions tested, mAb Lead-A formed smaller, lessheterogeneous complexes with Protein Y than mAb Lead-B (FIGS. 4A-4C,Tables 3-5).

TABLE 3 Approximate molar mass and retention time for mAb:Protein Ycomplexes. Peak 1 Peak 2 [Intact A [Intact ntibody]₁: Antibody]₂: Peak 3Molar [ProteinY]₂ [ProteinY]₃ Higher Order Ratio Complex ComplexComplexes Sample (mol:mol) R_(t), min M_(w), kDa R_(t), min M_(w), kDaR_(t), min M_(w), kDa Lead-A: 1:3 10.1 215.9 NA NA 13.1 ~500-1000ProteinY Lead-B: 1:3 10.1 219.1 12.5 390.1 14.3 ~550-2000 ProteinYR_(t): Retention Time; M_(w): weight average molar mass; NA: NotApplicable; min: minutes; kDa: kiloDaltons;

TABLE 4 Approximate molar mass and retention time for mAb:Protein Ycomplexes. Peak 1 Peak 2 Peak 3 [Intact [Intact [Intact Antibody]₂:Antibody]₂₋₃: Antibody]₄: Peak 4 Molar [ProteinY]₁₋₂ [ProteinY]₃₋₄[ProteinY]₃ Higher Order Ratio Complex Complex Complex Complexes Sample(mol:mol) R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w),kDa R_(t), min M_(w), kDa Lead-A: 1:1 11.9 347.7 13.5 589.4 NA NA 16.5~850- ProteinY 1400 Lead-B: 1:1 NA NA 14.0 448.7 15.3 635.9 16.4 ~815-ProteinY 2300 R_(t): Retention Time; M_(w): weight average molar mass;NA: Not Applicable; min: minutes; kDa: kiloDaltons;

TABLE 5 Approximate molar mass and retention time for mAb:Protein Ycomplexes. Peak 1 [Intact Antibody]₂:[ProteinY]₁ Peak 2 Molar RatioComplex Higher Order Complexes Sample (mol:mol) R_(t), min M_(w), kDaR_(t), min M_(w), kDa Lead-A:ProteinY 3:1 11.3 265.3 13.0 ~400-900 Lead-B:ProteinY 3:1 11.6 306.9 12.9 ~480-1600 Rt: Retention Time; Mw:weight average molar mass; NA: Not Applicable; min: minutes; kDa:kiloDaltons;

The size and heterogeneity of anti-Protein Y complexes correlated wellwith mouse PK observations (FIGS. 5A-5B). Larger complexes observed forLead-B with Protein Y correlated with faster clearance (FIG. 5B).

Example 3: Anti-Human Protein Z Complexes Methods

Sample Preparation

Samples were prepared in 1×DPBS, pH 7.4 and allowed to incubate at roomtemperature for 2 hrs. prior to fractionation of total protein byA4F-MALLS. The samples were as follows: 1 mM anti-Protein ZmAb1+Secondary mAb (0.5 mM+0.5 mM)+1 mM complement Protein Z (7combinations) or 1 mM anti-Protein Z mAb6+anti-Protein Z mAb7 (0.5mM+0.5 mM)+1 mM complement Protein Z. The list of secondary antibodiescan be found in Table 6.

TABLE 6 Sample Nomenclature. Nomenclature of Combo with Secondary mAbsTested anti-Protein Z mAb1 anti-Protein Z mAb2 mAb2 Combo anti-Protein ZmAb3 mAb3 Combo anti-Protein Z mAb4 mAb4 Combo anti-Protein Z mAb5 mAb5Combo anti-Protein Z mAb6 mAb6 Combo anti-Protein Z mAb7 mAb7 ComboCOMP1 mAb COMP1 Combo

A4F MALLS Analysis

All samples were incubated at ambient temperature for total of 2 hoursand maintained unfiltered at 4° C. prior to injection into an Eclipse™short channel fitted with a W350 spacer foil (350 μm spacer thickness,2.2 cm spacer width) and using a 4 kDa MWCO hydrophilic PES (PESH)membrane. The channel was pre-equilibrated with the mobile phase buffer(10 mM sodium phosphate, 500 mM sodium chloride, pH 7.0±0.1), prior tothe injection of each sample. BSA (2 mg/mL; 10 μg sample load) wasinjected separately and included as a system suitability control.

The fractionation method consisted of four steps: injection, focusing,elution, and a channel “wash-out” step. The A4F-MALLS mobile phasebuffer (10 mM sodium phosphate, 500 mM sodium chloride, pH 7.0±0.1) wasused throughout the fractionation method. Each sample (7 μg complex or 4μg individual component) was injected at a flow rate of 0.2 mL/min andfocused for 5 min with a focus flow rate of 1 mL/min. The sample waseluted with a channel flow rate of 1 mL/min with the linear gradientcross flow from 2 mL/min to 0 mL/min over 45 min. Finally, the crossflow was held at 0 mL/min for an additional 5 min to wash out thechannel. BSA was fractionated using the same parameter settings.

RBC Hemolysis Assay

Alternative pathway hemolysis assay was used as the measure ofcomplement activation to evaluate the ability of anti-Protein Z mAbs toblock the lysis of rabbit red blood cells (RbRBCs). Lysis of rabbit redblood cells by membrane attack complex is the basis of the assay bywhich complement activation is experimentally measured.

A desired number of RbRBCs are washed in GVB-Mg2+/EGTA buffer and resuspended at 2×10⁸ cells/ml. To test the efficacy of either singleanti-05 mAb or combination of anti-05 mAbs, normal human serum wasdiluted to 50-96% in GVB-Mg²⁺/EGTA buffer to achieve a finalconcentration of 25-48% when added to RBC. Round bottom 96 well plateswere used to measure hemolysis activity. A total of 100 ul RbRBCs (2×10⁸cells/ml) were plated into 96-well plate at 37° C. followed by additionof 100 ul of diluted serum. Cells were gently mixed and incubated at 37°C. for 30-120 minutes. After incubation time, the cells were spun downby centrifugation at 1250×g at 4° C. A total of 100 uL of thesupernatant was transferred to a fresh 96 flat bottom plate and read at412 nm on a Spectramax microplate reader. The calculation of percent ofhemolysis was done as described below.

The percentage of hemolysis was calculated with the absorbance values byusing the following equation:

$\begin{matrix}{{\%{Hemolysis}} = {100 \times \frac{\left( {{{Experimental}{Cell}{Lysis}} - {{Background}{Cell}{Lysis}}} \right)}{\left( {{{Maximum}{Cell}{Lysis}} - {{Background}{Cell}{Lysis}}} \right)}}} & {{Equation}3}\end{matrix}$

In this equation “background cell lysis” is the OD at A412 nm from thecells incubated in GVB-Mg²⁺/EGTA buffer only containing no serum. The“maximum cell lysis” is the OD at A412 nm from the cells treated withwater. Maximum inhibition of lysis was calculated as a differencebetween bottom and top values in the curve expressed as a percentage oftop value. Data represented as mean±Standard error of mean.

Results

Anti-Protein Z mAb1 (lead anti-Protein Z mAb) in combination with COMP1mAb or other Protein Z mAbs completely blocks hemolysis of rabbit RBCsvia alternative pathway activation (FIG. 6B, Table 8), compared tomonotherapies which do not completely block hemolysis (FIG. 6A, Table7). Because all of the anti-Protein Z mAb1:anti-Protein Z mAbcombinations completely blocked hemolysis of rabbit RBC, it was ofimportance to determine if there are differences in complex formation,such as size, shape and orientation which can provide insight into thepharmacokinetics (PK) of a mAb during drug development, such asimmunogenicity and/or target-mediated clearance.

TABLE 7 Effect of anti-Protein Z antibodies on rabbit RBC hemolysis. %Max Inh. ABPID AP, IC50 [M] AP, IC80 [M] of Lysis Anti-Protein Z mAb18.896e−008 1.970e−007 81.25 Anti-Protein Z mAb2 8.366e−008 1.813e−00788.66 Anti-Protein Z mAb3 5.252e−008 9.390e−008 59.24 Anti-Protein ZmAb4 4.942e−008 5.963e−008 36.63 Anti-Protein Z mAb5 7.419e−0081.467e−007 77.83 Anti-Protein Z mAb6 9.346e−008 2.260e−007 62.80Anti-Protein Z mAb7 7.424e−008 1.414e−007 76.21 COMP1 mAb 6.291e−0081.185e−007 61.14 COMP2 mAb 4.568e−008 5.600e−008 88.83

TABLE 8 Effect of anti-Protein Z antibody combinations on rabbit RBChemolysis. % Max Inh. ABPID AP, IC50 [M] AP, IC80 [M] of LysisAnti-Protein Z mAb1 + Anti- 7.182e−008 7.528e−008 97.59 Protein Z mAb2Anti-Protein Z mAb1 + Anti- 7.709e−008 8.749e−008 98.11 Protein Z mAb3Anti-Protein Z mAb1 + Anti- 9.751e−008 1.064e−007 98.16 Protein Z mAb4Anti-Protein Z mAb1 + Anti- 9.571e−008 1.051e−007 98.10 Protein Z mAb5Anti-Protein Z mAb1 + Anti- 7.737e−008 8.461e−008 97.29 Protein Z mAb6Anti-Protein Z mAb1 + Anti- 8.353e−008 9.432e−008 98.14 Protein Z mAb7Anti-Protein Z mAb1 + 7.372e−008 7.776e−008 98.26 COMP1 mAb Anti-ProteinZ mAb1 + 7.306e−008 8.017e−008 98.07 COMP2 mAb

In the absence of secondary mAbs, anti-Protein Z mAb1 formed canonical1:1 and 1:2 complexes with Protein Z when mixed in equimolar amounts(FIG. 7 , Table 9).

TABLE 9 Approximate molar mass and retention time for mAb:Protein Zcomplexes. Peak 1 Peak 2 [Intact Antibody]₁:[ProteinZ]₁ [IntactAntibody]₁:[ProteinZ]₂ Molar Ratio Complex Complex Sample (mol:mol)R_(t), min M_(w), kDa R_(t), min M_(w), kDa mAb1:ProteinZ 1:1 13.7 341.115.3 498.7 Rt: Retention Time; Mw: weight average molar mass; min:minutes; kDa: kiloDaltons;

Most secondary mAb combinations with anti-Protein Z mAb1 favoredsmaller, well defined complexes consistent with a heteromeric 2:2mAb:Protein Z complex (FIGS. 8 and 9 and Tables 10-12).

TABLE 10 Theoretical molar mass of mAb:Protein Z complex. TheoreticalmAb:Protein Z Molar Mass Complex (kDa) 1:0 150 0:1 195 1:1 345 2:1 4951:2 540 2:2 690 3:2 840 2:3 885 4:4 1380 6:6 2070

TABLE 11 Approximate molar mass and retention time for mAb:Protein Zcomplexes. Peak 1 Peak 2 Peak 3 [Intact [Intact [Intact Antibody]₂:Antibody]₄: Antibody]₆: Peak 4 Molar [ProteinZ]₂ [ProteinZ]₄ [ProteinZ]₆Higher Order Ratio Complex Complex Complex Complexes Sample (mol:mol)R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t),min M_(w), kDa mAb1:mAb5: 0.5:0.5:1 16.0 684.4 18.5 1342.4 20.1 1876.021.5 ~2250- ProteinZ 3560 mAb1:mAb7: 0.5:0.5:1 16.1 687.7 18.5 1327.420.1 1865.6 21.5 ~2380- ProteinZ 4250 R_(t): Retention Time; M_(w):weight average molar mass; min: minutes; kDa: kiloDaltons;

TABLE 12 Approximate molar mass and retention time for mAb:Protein Zcomplexes. Peak 1 Peak 2 Peak 3 [Intact [Intact [Intact Antibody]₂:Antibody]₄: Antibody]₆: Peak 4 Molar [ProteinZ]₂ [ProteinZ]₄ [ProteinZ]₆Higher Order Ratio Complex Complex Complex Complexes Sample (mol:mol)R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t),min M_(w), kDa mAb1:mAb3:ProteinZ 0.5:0.5:1 16.4 684.7 18.4 1261.8 NA NA20.2 ~1700- 2700 mAb1:mAb6:ProteinZ 0.5:0.5:1 15.7 685.9 17.7 1319.819.4 1849.8 20.6 ~2300- 3800 mAb6:mAb7:ProteinZ 0.5:0.5:1 15.8 687.717.8 1333.8 19.3 1871.6 20.6 ~2300- 3600

Although anti-Protein Z mAb1/anti-Protein Z mAb3 combination formedsimilar sized complexes with Protein Z, differences in elutiontime/profile suggested that complexes formed had differences inshape/orientation compared to other combinations (FIG. 9 ). Combinationsof anti-Protein Z mAb1 with anti-Protein Z mAb2 and COMP1 mAb favoredlarger, more heterogeneous complexes with Protein Z indicative of“paper-dolling” (FIG. 10 , Table 13).

TABLE 13 Approximate molar mass and retention time for mAb:Protein Zcomplexes. Peak 1 Peak 2 Peak 3 [Intact [Intact [Intact Antibody]₂:Antibody]₄: Antibody]₆: Peak 4 Molar [ProteinZ]₂ [ProteinZ]₄ [ProteinZ]₆Higher Order Ratio Complex Complex Complex Complexes Sample (mol:mol)R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t),min M_(w), kDa mAb1: 0.5:0.5:1 15.5 664.8 19.2 1304.3 21.9 1901.1 23.6~2300- mAb2: 4100 ProteinZ mAb1: 0.5:0.5:1 15.4 713.7 18.8 1346.1 21.52001.9 24.2 ~2500- COMP1: 5000 ProteinZ R_(t): Retention Time; M_(w):weight average molar mass; min: minutes; kDa: kiloDaltons;

Anti-Protein Z mAb4 combination with anti-Protein Z mAb1 displayed areduced tendency to form heteromeric complexes with Protein Z (FIG. 11 ,Table 14). Presence of free mAb and 1:1 mAb:Protein Z species indicatedincomplete formation of heteromeric complexes with Protein Z. Mixturesof homomeric and heteromeric complexes with Protein Z were also evident.

TABLE 14 Approximate molar mass and retention time for mAb:Protein Zcomplexes. Peak 1 Peak 2 [Intact [Intact Antibody]₂: Antibody]₄: Peak 3Molar [ProteinZ]₂ [ProteinZ]₄ Higher Order Ratio Complex ComplexComplexes Sample (mol:mol) R_(t), min M_(w), kDa R_(t), min M_(w), kDaR_(t), min M_(w), kDa mAb1:mAb4: 0.5:0.5:1 15.9 649.6 19.1 1288.2 20.6~1700- ProteinZ 2300 R_(t): Retention Time; M_(w): weight average molarmass; min: minutes; kDa: kiloDaltons;

Example 4: Order of Addition does not Significantly Impact the MolarMass and Distribution of Complexes Formed Between Anti-Protein Z mAb1,COMP1 mAb, and Protein Z Methods

To determine whether order of addition impacts complex formation,equimolar combinations of COMP1 mAb and Protein Z were prepared in1×DPBS, pH 7.4 to yield a molar ratio of 1 μM COMP1 mAb:1 μM Protein Zand allowed to incubate at ambient temperature for 1 hr. Followingincubation, varying amounts of Anti-Protein Z mAb1 was added to thepre-formed COMP1 mAb:Protein Z complexes and diluted in 1×DPBS, pH 7.4to yield the following molar ratios: 0.3 μM Anti-Protein Z mAb1:1 μMCOMP1 mAb:1 μM Protein Z, 1 μM Anti-Protein Z mAb1:1 μM COMP1 mAb:1 μMProtein Z, and 3 μM Anti-Protein Z mAb1:1 μM COMP1 mAb:1 μM Protein Z.and incubated for an additional hour prior to injection onto theinstrument. The A4F MALLS analysis methods of Example 3 were followed.

Results

Similar complexes, with respect to molar mass and distribution, wereformed between anti-Protein Z mAb1, COMP1 mAb, and Protein Z regardlessof whether anti-Protein Z mAb1 was added simultaneously (FIG. 12A, Table15) or sequentially (FIG. 12B, Table 15) to the other components. Theslight shift in elution time observed between the two datasets isindicative of the variability inherent to the method and is notconsidered unusual.

TABLE 15 Approximate molar mass and retention time for mAb:Protein Zcomplexes. mAb1: Peak 1 Peak 2 Peak 3 COMP1: [Intact [Intact [IntactProteinZ Antibody]₁: Antibody]₁: Antibody]₂₋₃: Peak 4 Molar [ProteinZ]₁[ProteinZ]₂ [ProteinZ]₂₋₃ Higher Ratio Complex Complex Complex OrderComplexes Sample (mol:mol) R_(t), min M_(w), kDa R_(t), min M_(w), kDaR_(t), min M_(w), kDa R_(t), min M_(w), kDa Simultaneous 3:1:1 NA NA14.5 536.6 16.7 888.6 18.0 ~1200-1950 Addition 1:1:1 NA NA 14.6 522.716.7 793.1 18.6 ~1400-2300 0.3:1:1 13.3 343.7 15.0 540.9 16.6 750.3 18.4~1000-1800 Sequential 3:1:1 NA NA 15.6 500.1 18.0 816.9 20.0 ~1200-1800Addition 1:1:1 NA NA 15.7 496.4 18.0 806.2 20.0 ~1500-2400 0.3:1:1 14.2379.8 16.4 662.7 17.9 817.8 19.9 ~1500-2600

Example 5: Anti-Protein W Complexes Methods

A4F-MALLS Mobile Phase Buffer

The mobile phase buffer (10 mM sodium phosphate, 500 mM sodium chloride,pH 7.0±0.1) was prepared by combining 1.4 g sodium phosphate monobasicmonohydrate, 10.7 g sodium phosphate dibasic heptahydrate, and 500 mL 5M sodium chloride; the solution was then brought to a volume to 5.0 Lwith HPLC grade water. The final measured pH of the buffer was 7.0. Themobile phase buffer was filtered (0.2 μm) before use.

A4F MALLS Analysis

The A4F-MALLS system was composed of an Eclipse™ 3+A4F Separation Systemcoupled to an Agilent 1200 Series HPLC system equipped with aultraviolet (UV) diode array detector, Wyatt Technology Dawn HELEOS® IIlaser light scattering instrument (LS), and an Optilab® T-rEXdifferential refractometer (RI) detector. The detectors were connectedin series in the following order: UV-LS-RI. LS and RI detectors werecalibrated according to instructions provided by Wyatt Technology.

Defined amounts of anti-Protein W mAb were each combined with Protein Wand diluted in 1×DPBS, pH 7.4 to yield the equimolar ratio: 1 μManti-Protein W mAb: 1 μM Protein W. All samples were incubated atambient temperature for 2 hours and maintained unfiltered at 4° C. priorto injection into an Eclipse™ short channel fitted with a W350 spacerfoil (350 μm spacer thickness, 2.2 cm spacer width) and using a 10 kDaMWCO regenerated cellulose membrane. The channel was pre-equilibratedwith the mobile phase buffer (10 mM sodium phosphate, 500 mM sodiumchloride, pH 7.0±0.1), prior to the injection of each sample. Bovineserum albumin (BSA; 2 mg/mL; 10 μg sample load) was injected separatelyand included as a system suitability control.

The fractionation method consisted of four steps: injection, focusing,elution, and a channel “wash-out” step. The A4F-MALLS mobile phasebuffer (10 mM sodium phosphate, 500 mM sodium chloride, pH 7.0±0.1) wasused throughout the fractionation method. Each sample (7 μg) wasinjected at a flow rate of 0.2 mL/min for 1 min and subsequently focusedfor 3 min with a focus flow rate of 1.0 mL/min. The sample was elutedwith a channel flow rate of 1.0 mL/min with the linear gradient crossflow from 3.0 mL/min to 0 mL/min over 25 min. Finally, the cross flowwas held at 0 mL/min for an additional 5 min to wash out the channel.BSA was fractionated using the same parameter settings.

Results:

A4F-MALLS was used to assess the relative size distribution of complexesformed between Protein W, a dimeric, multi-domain ligand, and severalanti-Protein W antibodies that specifically bind to different domainswithin the ligand. The theoretical molar mass and predictedstoichiometry of potential antibody complexes with Protein W areprovided in Table 16.

TABLE 16 Theoretical Molar Mass of mAb:Protein W Complexes. mAb:ProteinW Theoretical Complex Molar Mass (kDa) 1:0 146 0:1 146 1:1 292  1:2¹ 4382:2 584  2:3¹ 730 3:3 876  3:4¹ 1022 4:4 1168 ¹Unequal ratios (such as1:2 and 2:1) cannot be differentiated, because they will have same MW.

Overall, out of the panel of mAbs, mAb1 targeting Domain A formed thehighest proportion of lower-order complexes with the predominant speciesrepresenting a discrete 1:1 and 2:2 complex with Protein W when combinedat equimolar ratios (Peak 2, ˜289 kDa; and peak 3, ˜562 kDa, FIG. 13 ,Table 17).

TABLE 17 Molar Masses and Retention Time of Human Protein W Complexeswith mAb1 Targeting Domain A. Peak 2 Peak 3 Peak 4 Peak 5 Peak 1 [mAb]₁:[mAb]₂: [mAb]₃: Higher Order Molar Free mAb/ [Protein W]₁ [Protein W]₂[Protein W]₃ Heteromeric Ratio Protein W Complex Complex ComplexComplexes Sample (mol:mol) R_(t), min M_(w), kDa R_(t), min M_(w), kDaR_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w), kDaProteinW — 9.6 146.6 ND ND ND ND ND ND ND ND mAb1 — 9.5 145.1 ND ND NDND ND ND ND ND mAb1:Protein W 1:1 9.3 145.7 10.7 288.6 12.6 561.9 13.7823.9 14.5 ~1000- 2000 R_(t): Retention Time; M_(w): weight averagemolar mass; NA: Not Applicable; min: minutes; kDa: kiloDaltons;

Each of the mAbs targeting DomainB (mAb2, mAb3 and COMP1) predominantlyformed a discrete 2:2 complex with ProteinW (Peak 3, ˜563-580 kDa, FIG.14 , Table 18) with mAb2 and COMP1 forming the most homogeneousdistribution of complexes relative to other mAbs tested. While COMP2targeting DomainA primarily favored a mixture of 1:2 and 2:2 complexeswith ProteinW (Peak 3, ˜550 kDa, FIG. 15 , Table 19), a moderate degreeof large, heterogeneous complexes was also observed. This suggests thatunlike mAb1, which also targeted DomainA, COMP2 binds to a uniqueepitope on ProteinW that allows for the formation of extendedantibody-antigen lattices in a process termed “paper-dolling”. In thissample, a distinct peak (Peak 4) having a molar mass of approximately835 kDa was observed, followed by a series of broad, poorly-resolvedspecies (peak 5) with a wide molar mass distribution ranging from˜1000-1900 kDa (FIG. 15 , Table 19).

TABLE 18 Molar Masses and Retention Time of Human Protein W Complexeswith mAbs targeting the Domain B. Peak 2 Peak 3 Peak 4 Peak 5 Peak 1[mAb]₁: [mAb]₂: [mAb]₃: Higher Order Molar Free mAb/ [ProteinW]₁[ProteinW]₂ [Protein W]₃ Heteromeric Ratio Protein W Complex ComplexComplex Complexes Sample (mol:mol) R_(t), min M_(w), kDa R_(t), minM_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w),kDa Protein W — 9.6 146.6 ND ND ND ND ND ND ND ND mAb2 — 9.6 152.1 ND NDND ND ND ND ND ND mAb2:ProteinW 1:1 9.4 144.4 10.9 282.5 13.2 574.2 13.9731.3 15.4 ~1000- 1900 mAb3:ProteinW 1:1 9.3 144.1 10.7 267.8 12.9 562.514.0 830.5 14.6 ~1000- 1900 COMP1:ProteinW 1:1 9.4 143.1 10.8 298.3 13.0580.1 13.9 764.7 15.0 ~1000- 1900 R_(t): Retention Time; M_(w): weightaverage molar mass; NA: Not Applicable; min: minutes; kDa: kiloDaltons;

TABLE 19 Molar Masses and Retention Time of Human Protein W Complexeswith COMP2 targeting Domain A. Peak 3 Peak 4 Peak 5 Peak 1 [mAb]₁₋₂:[mAb]₂₋₃: Higher Order Molar Free Peak 2 [ProteinW]₂ [Protein W]₃Heteromeric Ratio Protein W Free mAb Complex Complex Complexes Sample(mol:mol) R_(t), min M_(w), kDa R_(t), min M_(w), kDa R_(t), min M_(w),kDa R_(t), min M_(w), kDa R_(t), min M_(w), kDa Protein W — 9.6 146.6 NDND ND ND ND ND ND ND COMP2 — 10.5 121.9 ND ND ND ND ND ND ND NDCOMP2:ProteinW 1:1 ND ND 9.4 147.1 13.1 550.2 15.2 835.1 16.9 ~1000-1900 R_(t): Retention Time; M_(w): weight average molar mass; NA: NotApplicable; min: minutes; kDa: kiloDaltons;

Based on the calculated molar masses of the individual components, peak4 likely represents complexes containing at least 3 molecules of mAbcoordinating 2-3 molecules of Protein W, whereas peak 5 corresponds to aheterogeneous distribution of higher order heteromeric complexescomposed of ≥3 molecules of mAb coordinating ≥4 molecules of Protein W(Table 18). In contrast, mAbs targeting Domain C (mAb4 and COMP3) formeda broad distribution of large, heterogeneous complexes (molar massranging from −0.700-8000 kDa) with mAb4 displaying the most extensive“paper-dolling” amongst the panel of mAbs tested (FIG. 16 , Table 20).

TABLE 20 Molar Masses and Retention Time of Human ProteinW Complexeswith mAbs targeting Domain C. Peak 2 Peak 3 Peak 1 [mAb]₁₋₂: HigherOrder Molar Free mAb/ [Protein W]₂ Heteromeric Ratio Protein W ComplexComplexes Sample (mol:mol) R_(t), min M_(w), kDa R_(t), min M_(w), kDaR_(t), min M_(w), kDa Portein W — 9.6 146.6 ND ND ND ND mAb4 — 9.5 148.3ND ND ND ND mAb4:Protein W 1:1 9.5 157.7 ND ND 28.5 1400- 4000COMP3:ProteinW 1:1 9.7 161.3 13.9 528.4 14.6 700- 8000

While in the foregoing specification this invention has been describedin relation to certain embodiments thereof, and many details have beenput forth for the purpose of illustration, it will be apparent to thoseskilled in the art that the invention is susceptible to additionalembodiments and that certain of the details described herein can bevaried considerably without departing from the basic principles of theinvention.

All references cited herein are incorporated by reference in theirentirety. The present invention may be embodied in other specific formswithout departing from the spirit or essential attributes thereof and,accordingly, reference should be made to the appended claims, ratherthan to the foregoing specification, as indicating the scope of theinvention.

We claim:
 1. A method for assessing the stoichiometry and sizedistribution of protein complexes in a sample, comprising: fractionatingthe sample by asymmetrical flow field flow fractionation (A4F); anddetermining the molar mass, stoichiometry, and size distribution of theprotein complexes in the sample using Multi-Angle Laser Light Scattering(MALLS), wherein the heterogeneous complexes consist of heterogeneousantibody:ligand complexes or heterogeneous fusion protein:ligandcomplexes.
 2. The method of claim 1, wherein the ligand is a solubleligand.
 3. The method of claim 1, wherein the antibody is a monoclonalantibody or an antigen binding fragment thereof.
 4. The method of claim1, wherein the antibody is a bispecific antibody or an antigen bindingfragment thereof.
 5. A method for selecting a lead protein drug productcomprising: adding a first protein drug product to a first samplecomprising a target of the first protein drug product to produceheterogeneous protein:ligand complexes; adding a second protein drugproduct to a second sample containing the same target to formprotein:ligand complexes; separating the heterogeneous protein:ligandcomplexes and determining the size distribution and stoichiometry ofheterogeneous protein:ligand complexes using Asymmetrical flow fieldflow fractionation—Multi-Angle Laser Light Scattering; and selecting theprotein drug product that forms fewer protein:ligand complexes as thelead target protein drug.
 6. The method of claim 5, wherein the proteindrug product that is selected forms fewer protein drug product complexeshaving a ratio protein drug product to ligand of 3:2, 2:3, 4:4, 6:6, or[2:2]_(n).
 7. The method of claim 5, wherein the ligand is a solubleligand.
 8. The method of claim 5, wherein the protein drug product is anantibody or antigen binding fragment thereof, a fusion protein, or arecombinant protein.
 9. The method of claim 5, wherein the protein drugproduct that is selected forms protein drug product complexes having aprotein drug product to ligand ratio selected from the group consistingof 1:0, 0:1, 1:1, 1:2, and 2:1.
 10. A pharmaceutical compositioncomprising the lead protein drug product selected according to claim 5.11. A method for characterizing protein complexes formed between aprotein drug product and its ligand comprising: combining the proteindrug product and its ligand in a solution to form a sample comprisingprotein drug product:ligand complexes; fractionating the sample usingasymmetrical flow-field flow fractionation; and subjecting thefractionated protein drug product:ligand complexes to multi-angle laserlight scattering to characterize the stoichiometry and size of proteindrug product:ligand complexes.